MCP server to access live ECHA CHEM database

• Dinh Long Huynh
  Uppsala University Uppsala University

  Pharmaceutical Biosciences Pharmaceutical Biosciences

starbase is a web-based application that provides various analytical and visualization tools for exploring large eukaryotic transposable elements known as Starships.

• Adrian Forsythe
  Uppsala University Uppsala University

  Organismal Biology Organismal Biology

PLATO estimates relapse risk after colorectal cancer liver metastasis, building on validated risk scores. PLATO is based on logistic regression models that translate the risk classes from published scores into a continuous percentage risk of relapse, providing a clinically meaningful output.

• Annika Viljamaa
  Karolinska Institutet Karolinska Institutet

  Clinical Science, Intervention and Technology Clinical Science, Intervention and Technology

Librarian is an open-access, web-based application for building and sharing high-quality MS² spectral libraries for nontarget high-resolution mass spectrometry. It provides a streamlined, end-to-end workflow to retrieve and harmonize chemical metadata from PubChem, design compound mixtures for HRMS acquisition, and assemble standardized, metadata- ... rich MS² records ready for deposition in public repositories such as MassBank. Designed to lower technical barriers, Librarian is modular, interoperable with common HRMS preprocessing tools, and supports scalable, community-driven expansion of open spectral libraries for metabolomics, exposomics, and environmental research. See more

• Stefano Papazian
  Stockholms University Stockholms University,SciLifeLab

  Environmental Science Environmental Science,National Facility for Exposomics, SciLifeLab Metabolomics & Exposomics Platform

Description: Interactive tool for assigning L-probe barcode codebooks, generating Opentrons robot input files, validating robot instructions, and visualizing barcode pipetting paths.

• Marco Grillo
  Stockholms University Stockholms University

  Biochemistry and Biophysics (DBB) Biochemistry and Biophysics (DBB)

Prediction of plasmid host range

• David Lund
  Chalmers University of Technology Chalmers University of Technology

  Mathematical Sciences Mathematical Sciences

Cell proliferation underpins organ formation, yet how spatio-temporal expansion of lymphatic endothelial cells (LECs) is controlled remains unclear. In this study, we used single-cell transcriptomic analysis at four different timepoints to determine genes that are enriched in proliferating LECs. Single-cell RNA-seq data were performed on LECs and ... venous endothelial cells (VECs) isolated by fluorescence-activated cell sorting of double-positive Tg(fli1a:nEGFP)y7;Tg(-5.2lyve1b:DsRed2)nz101 cells from zebrafish embryos at 36 hours post-fertilisation (hpf), 48 hpf, 5 days post-fertilisation, and 7 dpf. These timepoints represent the immature LEC progenitors to differentiated functional LECs lining the lumen of lymphatic vessels. This analysis identified genes forming a unique LEC proliferation code activated during bursts of LEC proliferation. We further functionally validated that lbr, fkbp1ab, and armc1l, LEC proliferation code components, play a role in lymphatic progenitor expansion, and that the code is conserved in mammals. This study is currently available as a preprint: Marleen Gloger, Marle Kraft, Di Peng et al. Lineage-enriched cell proliferation code underlies spatio-temporal regulation of cell cycle dynamics in lymphatic vessels, 11 March 2026, PREPRINT (Version 1) available at Research Square [https://doi.org/10.21203/rs.3.rs-5333191/v1] See more

• Kaska Koltowska
  Uppsala University Uppsala University

  Immunology, Genetics and Pathology Immunology, Genetics and Pathology

Interactive results and visualization UI interface for a swedish adaptation of FinnPRIO - a model for ranking plant pests based on risk

• Niklas Björklund
  Swedish University of Agricultural Sciences Swedish University of Agricultural Sciences

  Ecology Ecology

Given either: a nucleotide FASTA (genome/transcriptome), or a precomputed protein FASTA, and a table of epitope peptide sequences, the tool: Optionally generates a 6-frame translation (3 forward + 3 reverse-complement frames). Scans translated/protein sequences for exact epitope matches. Writes hit tables for downst ... ream analysis. . See more

• Marco Grillo
  Stockholms University Stockholms University

  Biochemistry and Biophysics (DBB) Biochemistry and Biophysics (DBB)

Dashboard plotting the number of people in Sweden aged 0-19 who have have filled a prescription for ADHD medications each year.

• Arnold Kochari
  Uppsala University Uppsala University,SciLifeLab

  Genetics, Immunology, and Pathology Genetics, Immunology, and Pathology,SciLifeLab Data Centre

This app allows users to input an image (in jpeg format) of a flower and get a prediction on what type of flower it is from a machine learning model. Top three most likely flower types according to the model’s prediction are shown.

• Arnold Kochari
  Uppsala University Uppsala University,SciLifeLab

  Genetics, Immunology, and Pathology Genetics, Immunology, and Pathology,SciLifeLab Data Centre

Reading public data from an online repository is not a big challenge, although doing so programmatically is perhaps not everyone's cup-of-tea. Likewise, setting up a Shiny app or similar on a hosting platform is simple enough for the digitally well-versed, but an insurmountable obstacle for the digitally inexperienced researcher. In this talk I w ... ill therefore present part of the KTH Digital Research Handbook that demonstrates how to setup a Shiny app on the ready-to-use platform SciLifeLab Serve and one way to configure it to semi-dynamically ingest data from a public dataset previously published on the KTH Data Repository, thus illustrating how sharing data openly makes reuse possible. See more

• Taha Ahmed
  KTH Royal Institute of Technology KTH Royal Institute of Technology

  University Library University Library

ShinyCell app for Axolotl limb regeneration single-cell RNA-seq time course data.

• Nicholas Leigh
  Lund University Lund University

  Faculty of Medicine Faculty of Medicine

A Shiny webapp for creating a Seurat object without programming expertise. Load a count matrix directory, interactively filter on metadata, view results, download Seurat object and results of differential gene expression testing.

• Rasmus Olofzon
  Lund University Lund University

  Lund Stem Cell Center Lund Stem Cell Center

Allows users to either upload an image file or take a picture using their webcam and get a prediction the chemical structure depicted in the image in SMILES notation.

• Arnold Kochari
  Uppsala University Uppsala University,SciLifeLab

  Genetics, Immunology, and Pathology Genetics, Immunology, and Pathology,SciLifeLab Data Centre

This dashboard visualises the spread of COVID-19 in Sweden: confirmed cases, ICU admissions, and deaths between February 2020 and March 2023.

• Arnold Kochari
  Uppsala University Uppsala University,SciLifeLab

  Genetics, Immunology, and Pathology Genetics, Immunology, and Pathology,SciLifeLab Data Centre

Hosting page for AntiMicRobial KG and prediction models.

• Leonie von Berlin
  Fraunhofer Institute for Translational Medicine and Pharmacology Fraunhofer Institute for Translational Medicine and Pharmacology

The alpha-beta-methylome web application is a comprehensive open resource based on the whole genome bisulfite sequencing and RNA-seq data from sorted human pancreatic islet α- and β-cells included in Cell-specific DNA methylation in human alpha and beta cells regulates gene expression in type 2 diabetes. alpha-beta-methylome lets the user explore ... cell type-, T2D-, age-, and sex-associations in DNA methylation and gene expression. See more

• Axel Lindström
  Lund University Lund University

  Clinical Sciences, Malmö Clinical Sciences, Malmö

Build leakage-free Drug-Target Affinity datasets from ChEMBL and train Graph Neural Networks for target-specific binding affinity prediction

• Gökhan Özsari
  Chalmers University of Technology Chalmers University of Technology

  Chalmers e-Commons Chalmers e-Commons

Interactive Shiny application accompanying the manuscript “Organ-specific proteomic aging predicts multimorbidity in twins”. The app allows exploration of organ-specific proteomic aging clocks, baseline associations, prevalent disease profiles, and incident outcomes using population-level and within-pair twin analyses.

• Hampus Hagelin
  Karolinska Institutet Karolinska Institutet

  MEB MEB

Single cell RNA-seq explorer for Il10ko chronic colitis in mouse

• Jennifer Fransson
  Uppsala University Uppsala University

  Cell and Molecular Biology Cell and Molecular Biology

Single cell RNA-seq explorer for CD45RBhi chronic colitis in mouse

• Jennifer Fransson
  Uppsala University Uppsala University

  Cell and Molecular Biology Cell and Molecular Biology

AI Agent that autonomously plans and executes data-driven workflows related to Drug Repurposing. It combines autonomous research, data extraction, knowledge graph construction, and analytical reasoning, featuring a long-term memory that enhances the system over time.

• Dinh Long Huynh
  Uppsala University Uppsala University

  Pharmaceutical Biosciences Pharmaceutical Biosciences

Where do your citations come from? Citation-Constellation: a free, open-source, no-code, and auditable tool for citation network decomposition with complementary BARON and HEROCON scores

• Mahbub Ul Alam
  Uppsala University Uppsala University,SciLifeLab

  Immunology, Genetics and Pathology Immunology, Genetics and Pathology,Data Centre

This app provides information on how proteins are related to plasma metabolites. It is a companion Atlas to the research article "When the Proteome Meets the Metabolome - Observational and Mendelian Randomization Analyses" published in Metabolism.

• Mario Delgado-Velandia
  Uppsala University Uppsala University

  Medical Sciences Medical Sciences

IFCB Plankton Classifier is a web application that automates phytoplankton image classification using a ResNet-50 model trained on the SMHI IFCB Plankton Image Reference Library and NIVA datasets. It combines single-image inference, large-scale batch processing, and threshold-aware prediction visualisation to streamline marine plankton analysis wo ... rkflows. See more

• Anders Torstensson
  Swedish Meteorological and Hydrological Institute Swedish Meteorological and Hydrological Institute

A frontface to EU-OpenScreen Impulse

• Bishab Pokharel
  Fraunhofer Institute for Translational Medicine and Pharmacology Fraunhofer Institute for Translational Medicine and Pharmacology

OlinkWrapper provides a user-friendly interface for performing quick analysis of Olink data using OlinkAnalyze package. It allows for data upload, parameter customization, visualization of results, and exporting of analysis outputs.

• Jyotirmoy Das
  Linköping University Linköping University

  Biomedical and Clinical Sciences Biomedical and Clinical Sciences

LymphMutSig is an interactive platform that provides a comprehensive atlas of mutational signatures in B-cell cancers and enables user-driven mutational signature analysis of B-cell cancer genomic data.

• Hui Wan
  Karolinska Institutet Karolinska Institutet

  Medical Biochemistry and Biophysics, Immunology Medical Biochemistry and Biophysics, Immunology

5PSeq is a method for profiling 5' phosphorylated mRNA undergoing decay. Degradation coincides with translation, as the enzymatic cleavage of the 5' end of mRNAs occurs right behind the last trailing ribosome. Therefore, information about ribosome dynamics can be obtained by profiling the degradome (5PSeq). 5PSeq Explorer is a web application tha ... t allows the visualisation of preprocessed co-translational degradation intermediates datasets in bacteria, Saccharomyces and Candida albicans in response to various stresses and drug treatments. Information about frame usage, translation start and termination sites, amino acid and codon usage is available. See more

• Irene Stevens
  Karolinska Institutet Karolinska Institutet,SciLifeLab

  MTC MTC

Tools for normalization, evaluation of outliers, technical biases and batch effects and differential expression analysis.

• Måns Zamore
  LTH Lund University LTH Lund University

  Immunotechnology Immunotechnology

Chromatin interaction database for b-cell precursor acute lymphoblastic leukemia

• Minjun Yang
  Lund University Lund University

  Laboratory Medicine Laboratory Medicine

Results from surveys of Swedish researchers' and ethics reviewers' attitudes towards research misconduct (RM) and questionable research practices (QRPs).

• Amanda Lindkvist
  Linköping University Linköping University

  Economics Economics

molecular epidemiology toolbox

• Yingxiao Yan
  Stockholms University Stockholms University

  environmental science environmental science

An web application for MAF format cancer mutation profiles analysis and visualizations.

• Xiya Song
  KTH Royal Institute of Technology KTH Royal Institute of Technology

  Protein Science Protein Science

PKSmart is an open-source app framework built specifically for predicting human and animal PK parameters

• Ola Spjuth
  Uppsala University Uppsala University

  Pharmaceutical Biosciences Pharmaceutical Biosciences

DICTrank Predictor is an open-source app framework built specifically for human drug-induced cardiotoxicity (DICT).DICTrank Predictor employs physicochemical parameters as feature. For more details look at https://www.biorxiv.org/content/10.1101/2023.10.15.562398v1

• Ola Spjuth
  Uppsala University Uppsala University

  Pharmaceutical Biosciences Pharmaceutical Biosciences

DILI Predictor is an open-source app framework built specifically for human drug-induced liver injury (DILI). DILI Predictor employs eleven proxy-DILI labels from in vitro and in vivo datasets along with pharmacokinetic parameters, structural fingerprints and physicochemical parameters as features.

• Ola Spjuth
  Uppsala University Uppsala University

  Pharmaceutical Biosciences Pharmaceutical Biosciences

KG Generator app under KGG in Data Science Toolkit

• Bishab Pokharel
  Fraunhofer Institute for Translational Medicine and Pharmacology Fraunhofer Institute for Translational Medicine and Pharmacology

A resource of validated and annotated gene fusions in cancer cell lines

• Helena Persson
  Lund University Lund University

  Clinical Sciences Lund Clinical Sciences Lund

MCP server for SPECS dataset. It can connect to any MCP client, such as LLM, AI Agents, etc.

• Dinh Long Huynh
  Uppsala University Uppsala University

  Pharmaceutical Biosciences Pharmaceutical Biosciences

Dashboard for the R4A Expertise KG

• Leonie von Berlin
  Fraunhofer Institute for Translational Medicine and Pharmacology Fraunhofer Institute for Translational Medicine and Pharmacology

Fallback app of datascience toolkit

• Leonie von Berlin
  Fraunhofer Institute for Translational Medicine and Pharmacology Fraunhofer Institute for Translational Medicine and Pharmacology

An education tools for students to learn PKPD Modelling

• Dinh Long Huynh
  Uppsala University Uppsala University

  Pharmaceutical Biosciences Pharmaceutical Biosciences

This is an interactive Shiny-based app that visualises the analysed data for CRISPR screens using the PbHiT system in the rodent malaria parasite Plasmodium berghei as described in Jonsdottir et al. 2024 generated by the Bushell lab (www.bushelllab.com/) at Umeå University

• Johan Henriksson
  Umeå University Umeå University

  Molecular Biology Molecular Biology

A shiny application to process OLINK data. Outlier detection - filtering - statistical analysis - visualization - publication ready figures all at one place.

• Debojyoti Das
  Linköping University Linköping University

  Biomedical and Clinical Sciences (BKV) Biomedical and Clinical Sciences (BKV)

gsalit is a user-friendly Streamlit application that allows researchers to run the Illumina GSA (Global Screening Array) genotyping pipeline without manually handling command-line tools. A second version, built with Python and Conda, and available via Bioconda.

• Jyotirmoy Das
  Linköping University Linköping University

  Biomedical and Clinical Sciences Biomedical and Clinical Sciences

This application: XPS Files: Converts XPS to PDF using xpstopdf (requires libgxps-utils) PDF Files: Extracts tables using advanced table detection Number Format: Handles Swedish format (comma as decimal separator) Table Merging: Automatically merges fragmented tables from multiple pages Excel Export: Saves each file's tables to separate Exc ... el sheets Summary: Optionally creates a combined summary with Sample, ng/ul, and 260/280 data Supported formats: PDF files with tables XPS files (converted to PDF first) Output: Individual Excel files for each input file Combined summary Excel file (optional) ZIP download for multiple files See more

• Johannes Roylands
  LTH Lund University LTH Lund University

  Immunology, Genetics and Pathology Immunology, Genetics and Pathology

ThermoTargetMiner is an interactive Shiny application that enables simplified visualization and exploration of drug–target relationships derived from the Proteome Integral Solubility Alteration (PISA) assay. The app integrates processed data from 67 approved drugs and candidate compounds tested in lung cancer cell lines, providing users with tools ... to: · Visualize proteome-wide solubility shifts in lysate and living lung cancer cells. · Identify and compare targets across different drugs and conditions. · Retrieve a structured list of discovered targets for each compound. By combining intuitive data handling with accessible visualization, ThermoTargetMiner serves as a practical resource for researchers interested in drug target discovery and mechanism-of-action studies in lung cancer. See more

• Hezheng Lyu
  Karolinska Institutet Karolinska Institutet

  Medical Biochemistry and Biophysics Medical Biochemistry and Biophysics

HDAnalyzeR-app is a graphical interface for HDAnalyzeR R-package developed by the Human Disease Blood Atlas. The goal is to simplify data analysis for biomarker discovery in disease research. With HDAnalyzeR, you can easily perform tasks like protein differential expression analysis, classification modeling, dimensionality reduction and data visua ... lization. See more

• Konstantinos Antonopoulos
  KTH Royal Institute of Technology KTH Royal Institute of Technology

  Protein Science Protein Science

lipidomics

• Vikash Pandey
  Umeå University Umeå University

  Molecular Biology Molecular Biology

Data browser showing peptide-level mass spectrometry proteome associations with affinity proteomics

• Isabelle Leo
  Karolinska Institutet Karolinska Institutet

  OnkPat OnkPat

A single shiny solution from sequencer data to pathway analysis

• Jyotirmoy Das
  Linköping University Linköping University

  Biomedical and Clinical Sciences Biomedical and Clinical Sciences

CitizenScience Project

• Nanjiang Shu
  Uppsala University Uppsala University,SciLifeLab

  Cell and Molecular Biology Cell and Molecular Biology,National Bioinformatics Infrastructure Sweden

Related publication: Andersson, Axel, et al. "Points2Regions: Fast, interactive clustering of imaging‐based spatial transcriptomics data." Cytometry Part A 105.9 (2024): 677-687. https://doi.org/10.1002/cyto.a.24884

• Christophe Avenel
  Uppsala University Uppsala University

  Information Technology Information Technology

Predicts Ames Mutagenicity for a chemical structure using an SVM model with Signatures features via the CPSign modeling tool.

• Ola Spjuth
  Uppsala University Uppsala University

  Pharmaceutical Biosciences Pharmaceutical Biosciences

It helps to calculate sequencing depth required to get microbial genomes from metagenomics

• Lokeshwaran Manoharan
  Lund University Lund University

  NBIS, Faculty of Medicine NBIS, Faculty of Medicine

The Multifunctional Potential and Cost Matrix provides an integrated assessment of the benefits and costs of urban blue-green infrastructure (BGI) elements. Firstly, the potential to provide three functions: urban stormwater management, heat stress reduction and recreation, is assessed based on scientific evidence. Secondly, the combined performan ... ce across these three functions, i.e. the multifunctionality potential, is related to costs of initial construction and long-term maintenance to support planning decisions. See more

• Nils Wallenberg
  Göteborgs University Göteborgs University

  Earth Sciences Earth Sciences

API for KGG

• Leonie von Berlin
  Fraunhofer Institute for Translational Medicine and Pharmacology Fraunhofer Institute for Translational Medicine and Pharmacology

CAPIM is an integrative computational pipeline for identifying and characterizing catalytic sites in proteins. It combines enzymatic activity prediction, pocket detection, and ligand docking simulations to determine active residues and annotate them with Enzyme Commission (EC) numbers computationally. CAPIM supports multi-chain protein structures, ... making it suitable for comprehensive enzymatic analysis in complex biological systems. See more

• Gökhan Özsari
  Chalmers University of Technology Chalmers University of Technology

  Chalmers e-Commons Chalmers e-Commons

enrichedmassspec - a shiny app to visualize differentially expressed proteins (DEPs) and carry out enrichment analysis using different methods on Mass Spectrometry data from generated using spectronaut

• Debojyoti Das
  Linköping University Linköping University

  Biomedical and Clinical Sciences (BKV) Biomedical and Clinical Sciences (BKV)

This app provides a reference database of proteins found in dried blood spots, based on published scientific studies. It serves as a tool for exploring the dried blood spot proteome.

• William Stauch
  KTH Royal Institute of Technology KTH Royal Institute of Technology

  Protein Science Protein Science

This app provides complementary visualizations of affinity proteomics data generated from dried blood spot (DBS) samples collected from a mouse model. The visualizations present longitudinal protein profiles in infected and uninfected mice, heatmaps of protein-protein correlations, and data quality assessments.

• Annika Bendes
  KTH Royal Institute of Technology KTH Royal Institute of Technology

  Protein Science Protein Science

Suite of data science tools made by Fraunhofer ITMP

• Leonie von Berlin
  Fraunhofer Institute for Translational Medicine and Pharmacology Fraunhofer Institute for Translational Medicine and Pharmacology

Drug Likeness Assessment app under KGG in Data Science Toolkit

• Bishab Pokharel
  Fraunhofer Institute for Translational Medicine and Pharmacology Fraunhofer Institute for Translational Medicine and Pharmacology

KG Visualizer app under KGG in Data Science Toolkit

• Bishab Pokharel
  Fraunhofer Institute for Translational Medicine and Pharmacology Fraunhofer Institute for Translational Medicine and Pharmacology

peak cluster

• Vikash Pandey
  Umeå University Umeå University

  Molecular Biology Molecular Biology

KISSE is a species search engine that utilizes collagen sequences from eight different species to identify unknown samples.

• Hassan Gharibi
  Karolinska Institutet Karolinska Institutet

  Medical Biochemistry and Biophysics Medical Biochemistry and Biophysics

The Chemical Biology Atlas (https://doi.org/10.1101/2025.07.23.666341) is an interactive online platform designed to facilitate the exploration of biological activities, mechanisms of action, and molecular targets associated with chemical compounds. Built on a Neo4j graph database, the Atlas enables intuitive navigation of complex relationships be ... tween molecules and biological entities. The current release is based on a harmonized library of 5,230 molecules from the Specs repurposing set, in collaboration with the Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP) and Karolinska Institute (KI). The database is built around publicly available annotations collected using the Chemical Annotator pipeline (https://github.com/REMEDI4ALL/chemical_annotator), ensuring comprehensive and standardized data integration. The Chemical Biology Atlas offers several search capabilities, network analysis, and dynamic visualization, allowing scientists to explore interactions, mechanisms, and repurposing opportunities in chemical biology. See more

• Flavio Ballante
  Karolinska Institutet Karolinska Institutet

  Medical Biochemistry and Biophysics Medical Biochemistry and Biophysics

New interventions to control malaria depend on a deep understanding of the parasite that causes the disease. The PlasmoGEM project produces free genetic tools for research on malaria parasites. We also use the reagents in genetic screens to identify parasite gene functions at scale. The purpose of this database is to share data generated by the p ... roject. See more

• Vikash Pandey
  Umeå University Umeå University

  Molecular Biology Molecular Biology

An app designed to explore the *Populus* transcriptome throughout a yearly growth cycle. POPUL-R is based on a RNA-Seq dataset we have obtained from different poplar tissues in outdoor and indoor conditions, published in Marcon et. al (2025). In this app, you can perform exploratory analyses on your genes of interest such as visualizing their exp ... ression profiles, identifying other genes with similar expression patterns, and exploring the biological processes they may be involved in. See more

• Laura García Romañach
  Swedish University of Agricultural Sciences Swedish University of Agricultural Sciences

  Forest Genetics and Plant Physiology Forest Genetics and Plant Physiology

Biome-specific gene catalogues have been recovered for many environments using shotgun metagenomics, followed by assembly and gene calling on the assembled contigs. We recently proposed a novel mix-assembly strategy, combining individual and co-assembly approaches, and used this approach to assemble an extensive non-redundant gene set from 124 Bal ... tic Sea metagenome samples. The Baltic Sea Gene Set (BAGS v1.1) comprises 66.53 million functionally and taxonomically annotated genes. To enable interactive exploration of this gene catalogue we have developed an RShiny application, BAGS-Shiny, that allows users to perform searches by sequence similarity (BLAST) and/or taxonomic and functional annotation. The gene catalogue and web application will serve as valuable tools for exploring microbial gene functions in brackish ecosystems. See more

• Anders Andersson
  KTH Royal Institute of Technology KTH Royal Institute of Technology,SciLifeLab

  Gene Technology Gene Technology

This site provides a databases of knockout designs targeting the entire Plasmodium berghei protein encoding genome using the PbHiT CRISPR system as described in Jonsdottir et al. DOI: https://doi.org/10.1101/2024.04.20.590404

• Johan Henriksson
  Umeå University Umeå University

  Molecular Biology Molecular Biology

Predicting chemical EC50 and EC10 ecotoxiticy values towards fish, aquatic invertebrate, and algae for a diverse set of effects using AI. Publication in Science Advances available through DOI: https://doi.org/10.1126/sciadv.adk6669

• Käll Styrbjörn
  Chalmers University of Technology Chalmers University of Technology

  Chalmers University of Technology Chalmers University of Technology

This predictive model distinguishes between Relapsing-Remitting Multiple Sclerosis (RRMS) and Secondary Progressive Multiple Sclerosis (SPMS) using electronic health records collected at each hospital visit, with a focus on identifying transitions from RRMS to SPMS. It incorporates Conformal Prediction (CP) to quantify uncertainty and integrates E ... xplainable AI (SHAP) to interpret the contribution of individual features to the predictions. The tool is in an anonymized form for research purposes. See more

• Akshai Parakkal Sreenivasan
  Uppsala University Uppsala University

  Medical Sciences, Clinical Chemistry Medical Sciences, Clinical Chemistry

**SNRApp** is an interactive web app to calculate the Signal-to-Noise Ratio (SNR) from spatial omics data. The user will need to upload an `anndata` and set the top and bottom percentile.

• Nima Rafati
  Uppsala University Uppsala University

  Medical Biochemistry and Microbiology Medical Biochemistry and Microbiology

Apical hook kinetics analyzer: Shiny app to quantify and visualize kinematics based on angle measurements of Arabidopsis thaliana dark-grown seedlings extracted from time-series.

• Adrien Heymans
  Swedish University of Agricultural Sciences Swedish University of Agricultural Sciences

  Forest Genetics and Plant Physiology Forest Genetics and Plant Physiology

TurgoLab is an interactive, FEM-based simulation app for inflating 2D cellular structures from .geo files. It integrates the BVPy framework to enable intuitive biomechanical modeling of plant tissues under turgor pressure from the geometry made with Anatomeshr .

• Adrien Heymans
  Swedish University of Agricultural Sciences Swedish University of Agricultural Sciences

  Forest Genetics and Plant Physiology Forest Genetics and Plant Physiology

TissUUmaps demo

• Christophe Avenel
  Uppsala University Uppsala University

  Information Technology Information Technology

A converter of 2D plant anatomical data into finite element mesh (GEO) format.

• Adrien Heymans
  Swedish University of Agricultural Sciences Swedish University of Agricultural Sciences

  Forest Genetics and Plant Physiology Forest Genetics and Plant Physiology

Visualizations of the results from an interaction screen of 215 G protein-coupled receptors (GPCRs) and the receptor activity–modifying proteins (RAMPs). Companion app to ‘Multiplexed mapping of the interactome of GPCRs with receptor activity–modifying proteins’, https://doi.org/10.1126/sciadv.ado9959

• Leo Dahl
  KTH Royal Institute of Technology KTH Royal Institute of Technology

  Protein Science, Biomedical Proteomics Protein Science, Biomedical Proteomics

Visualizations of the results from a selectivity screen of >400 antibodies targeting 215 G protein-coupled receptors (GPCRs). Companion app to ‘Multiplexed selectivity screening of anti-GPCR antibodies’, https://doi.org/10.1126/sciadv.adf9297

• Leo Dahl
  KTH Royal Institute of Technology KTH Royal Institute of Technology

  Protein Science, Biomedical Proteomics Protein Science, Biomedical Proteomics

ShinyCell app detailing cellular landscape of equine asthma

• Amanda Raine
  Uppsala University Uppsala University

  Medical Sciences Medical Sciences

Supplementary material to Sdougkou et al. 2024, "Longitudinal Exposomics in a Multiomic Wellness Cohort Reveals Distinctive and Dynamic Environmental Chemical Mixtures in Blood" Environmental Science & Technology, 58 (37) 16302–16315 https://doi.org/10.1021/acs.est.4c05235

• Stefano Papazian
  Stockholms University Stockholms University,SciLifeLab

  Environmental Science Environmental Science,National Facility for Exposomics, SciLifeLab Metabolomics & Exposomics Platform

Related publication: Li, Xiaofei, et al. "Profiling spatiotemporal gene expression of the developing human spinal cord and implications for ependymoma origin." Nature neuroscience 26.5 (2023): 891-901. https://doi.org/10.1038/s41593-023-01312-9

• Christophe Avenel
  Uppsala University Uppsala University

  Information Technology Information Technology

Related publication: Kukanja, Petra, et al. "Cellular architecture of evolving neuroinflammatory lesions and multiple sclerosis pathology." Cell 187.8 (2024): 1990-2009. https://doi.org/10.1016/j.cell.2024.02.030

• Christophe Avenel
  Uppsala University Uppsala University

  Information Technology Information Technology

Related publication: Andersson, Axel, et al. "Cell segmentation of in situ transcriptomics data using signed graph partitioning." International Workshop on Graph-Based Representations in Pattern Recognition. Cham: Springer Nature Switzerland, 2023. https://doi.org/10.1007/978-3-031-42795-4_13

• Christophe Avenel
  Uppsala University Uppsala University

  Information Technology Information Technology

Related publication: Ström, Peter, et al. "Artificial intelligence for diagnosis and grading of prostate cancer in biopsies: a population-based, diagnostic study." The Lancet Oncology 21.2 (2020): 222-232, https://doi.org/10.1016/S1470-2045(19)30738-7/

• Christophe Avenel
  Uppsala University Uppsala University

  Information Technology Information Technology

Explores interpretability for chest X-ray pathology predictions using methods—Grad-CAM, LIME, SHAP, and LRP. It provides heatmaps and evaluation metrics for better insights into the medical significance of predictions made by deep learning models.

• Mahbub Ul Alam
  Uppsala University Uppsala University,SciLifeLab

  Immunology, Genetics and Pathology Immunology, Genetics and Pathology,Data Centre

This is for exploring blood phenotypes in plasmogem screen data.

• Vikash Pandey
  Umeå University Umeå University

  Molecular Biology Molecular Biology

This Shiny app provides a user-friendly interface for performing Weighted Gene Co-expression Network Analysis (WGCNA) on RNA-seq/Microarray and DNA methylation (Array/Sequencing) data. It allows for data upload, parameter customization, visualization of results, and exporting of analysis outputs.

• Jyotirmoy Das
  Linköping University Linköping University

  Biomedical and Clinical Sciences Biomedical and Clinical Sciences

MMAtt-DTA: MultiModal Attention Drug-Target Affinity prediction

• Aleksandr Kushnir
  University of Helsinki University of Helsinki

  Public Health and Caring Sciences Public Health and Caring Sciences

Demo of Bayesian updating for teaching purposes. By Johan Henriksson, www.henlab.org. Source at https://github.com/henriksson-lab/demo_bayesupdate

• Johan Henriksson
  Umeå University Umeå University

  Molecular Biology Molecular Biology

Data exploration analysis tool. Load your csv data file and it will help to clean the data, report the missing/NA values (using pareto graph), perform a set of various statistical analyses (e.g., correlation, t-test, MW-test, KS-test, and more) resulting in tables and graphs.

• Ilona Szczot
  Linköping University Linköping University

  CSAN CSAN

Clusetering of phenotype data

• Vikash Pandey
  Umeå University Umeå University

  Molecular Biology Molecular Biology

Comparing 4 types of the most common reference populations for child sex- and age-adjusted Body Mass Index (BMI)

• Maja Engsner
  Uppsala University Uppsala University

  Medical Cell Biology Medical Cell Biology

Service that provides a REST Api to convert between different chemical notations. More info: https://github.com/DouglasConnect/ChemIdConvert.

• Hamza Saeed
  Uppsala University Uppsala University,SciLifeLab

  Immunology, Genetics and Pathology Immunology, Genetics and Pathology,SciLifeLab Data Centre

In-silico Drug Repurposing Catalogue REMEDi4ALL (iDRC-R4A).

• Aleksandr Kushnir
  University of Helsinki University of Helsinki

  Public Health and Caring Sciences Public Health and Caring Sciences

API for Predicting Off-Target Binding Profiles With Confidence Using Conformal Prediction. Refer to https://doi.org/10.3389/fphar.2018.01256 for the paper describing the tool.

• Hamza Saeed
  Uppsala University Uppsala University,SciLifeLab

  Immunology, Genetics and Pathology Immunology, Genetics and Pathology,SciLifeLab Data Centre

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• Christophe Avenel
  Uppsala University Uppsala University

  Information Technology Information Technology

IFNB single-cell transcriptomics data

• Roy Francis
  SciLifeLab SciLifeLab,Uppsala University

  National Bioinformatics Infrastructure Sweden National Bioinformatics Infrastructure Sweden, Cell and Molecular Biology

Trancriptom analysis for Suprcellfactories project

• Rasool Saghaleyni
  Chalmers University of Technology Chalmers University of Technology

  Systems and Synthetic Biology Systems and Synthetic Biology

scRNASeq of 55 samples from zebrafish brain. This project aims to characterize expression profile of different cell types.

• Nima Rafati
  Uppsala University Uppsala University

  Medical Biochemistry and Microbiology Medical Biochemistry and Microbiology

The Mouse Organ Metabolite Atlas

• Tomasz Czuba
  Lund University Lund University

  Clinical Sciences, Cardiology Clinical Sciences, Cardiology

Power analysis for RNA-Seq experiment. Estimate number of samples required and more.

• Roy Francis
  SciLifeLab SciLifeLab,Uppsala University

  National Bioinformatics Infrastructure Sweden National Bioinformatics Infrastructure Sweden, Cell and Molecular Biology

Companion resource to the article, 'An online atlas of human plasma metabolite signatures of gut microbiome composition' by Dekkers et al

• Koen Dekkers
  Uppsala University Uppsala University

  Medical Sciences, Molecular epidemiology Medical Sciences, Molecular epidemiology

Meta-analysis of skeletal muscle response to exercise and inactivity

• Nicolas Pillon
  Karolinska Institutet Karolinska Institutet

  Physiology and Pharmacology Physiology and Pharmacology

This app is part of the Drug Repurposing Encyclopedia (DRE), a web server for systematic drug repurposing across 20 organisms. Refer to https://doi.org/10.1101/2023.03.10.532084 for the paper describing the tool.

• Lu Pan
  Karolinska Institutet Karolinska Institutet

  Environmental Medicine Environmental Medicine

This app is part of the Drug Repurposing Encyclopedia (DRE), a web server for systematic drug repurposing across 20 organisms. Refer to https://doi.org/10.1101/2023.03.10.532084 for the paper describing the tool.

• Lu Pan
  Karolinska Institutet Karolinska Institutet

  Environmental Medicine Environmental Medicine

This app is part of the Drug Repurposing Encyclopedia (DRE), a web server for systematic drug repurposing across 20 organisms. Refer to https://doi.org/10.1101/2023.03.10.532084 for the paper describing the tool.

• Lu Pan
  Karolinska Institutet Karolinska Institutet

  Environmental Medicine Environmental Medicine

This app is part of the Drug Repurposing Encyclopedia (DRE), a web server for systematic drug repurposing across 20 organisms. Refer to https://doi.org/10.1101/2023.03.10.532084 for the paper describing the tool.

• Lu Pan
  Karolinska Institutet Karolinska Institutet

  Environmental Medicine Environmental Medicine

This app is part of the Drug Repurposing Encyclopedia (DRE), a web server for systematic drug repurposing across 20 organisms. Refer to https://doi.org/10.1101/2023.03.10.532084 for the paper describing the tool.

• Lu Pan
  Karolinska Institutet Karolinska Institutet

  Environmental Medicine Environmental Medicine

This app is part of the Drug Repurposing Encyclopedia (DRE), a web server for systematic drug repurposing across 20 organisms. Refer to https://doi.org/10.1101/2023.03.10.532084 for the paper describing the tool.

• Lu Pan
  Karolinska Institutet Karolinska Institutet

  Environmental Medicine Environmental Medicine

This app is part of the Drug Repurposing Encyclopedia (DRE), a web server for systematic drug repurposing across 20 organisms. Refer to https://doi.org/10.1101/2023.03.10.532084 for the paper describing the tool.

• Lu Pan
  Karolinska Institutet Karolinska Institutet

  Environmental Medicine Environmental Medicine

This app is part of the Drug Repurposing Encyclopedia (DRE), a web server for systematic drug repurposing across 20 organisms. Refer to https://doi.org/10.1101/2023.03.10.532084 for the paper describing the tool.

• Lu Pan
  Karolinska Institutet Karolinska Institutet

  Environmental Medicine Environmental Medicine

This app is part of the Drug Repurposing Encyclopedia (DRE), a web server for systematic drug repurposing across 20 organisms. Refer to https://doi.org/10.1101/2023.03.10.532084 for the paper describing the tool.

• Lu Pan
  Karolinska Institutet Karolinska Institutet

  Environmental Medicine Environmental Medicine

This app is part of the Drug Repurposing Encyclopedia (DRE), a web server for systematic drug repurposing across 20 organisms. Refer to https://doi.org/10.1101/2023.03.10.532084 for the paper describing the tool.

• Lu Pan
  Karolinska Institutet Karolinska Institutet

  Environmental Medicine Environmental Medicine

This app is part of the Drug Repurposing Encyclopedia (DRE), a web server for systematic drug repurposing across 20 organisms. Refer to https://doi.org/10.1101/2023.03.10.532084 for the paper describing the tool.

• Lu Pan
  Karolinska Institutet Karolinska Institutet

  Environmental Medicine Environmental Medicine

This app is part of the Drug Repurposing Encyclopedia (DRE), a web server for systematic drug repurposing across 20 organisms. Refer to https://doi.org/10.1101/2023.03.10.532084 for the paper describing the tool.

• Lu Pan
  Karolinska Institutet Karolinska Institutet

  Environmental Medicine Environmental Medicine

This app is part of the Drug Repurposing Encyclopedia (DRE), a web server for systematic drug repurposing across 20 organisms. Refer to https://doi.org/10.1101/2023.03.10.532084 for the paper describing the tool.

• Lu Pan
  Karolinska Institutet Karolinska Institutet

  Environmental Medicine Environmental Medicine

This app is part of the Drug Repurposing Encyclopedia (DRE), a web server for systematic drug repurposing across 20 organisms. Refer to https://doi.org/10.1101/2023.03.10.532084 for the paper describing the tool.

• Lu Pan
  Karolinska Institutet Karolinska Institutet

  Environmental Medicine Environmental Medicine

Single Protein Localization

• Luay Aswad
  Karolinska Institutet Karolinska Institutet,SciLifeLab

  Oncology-Pathology Oncology-Pathology

Correlation Network

• Luay Aswad
  Karolinska Institutet Karolinska Institutet,SciLifeLab

  Oncology-Pathology Oncology-Pathology

Heatmap

• Luay Aswad
  Karolinska Institutet Karolinska Institutet,SciLifeLab

  Oncology-Pathology Oncology-Pathology

Network

• Luay Aswad
  Karolinska Institutet Karolinska Institutet,SciLifeLab

  Oncology-Pathology Oncology-Pathology

Data Download

• Luay Aswad
  Karolinska Institutet Karolinska Institutet,SciLifeLab

  Oncology-Pathology Oncology-Pathology

Application that allows users to get predictive data about compound (Multiple Molecules)

• Hamza Saeed
  Uppsala University Uppsala University,SciLifeLab

  Immunology, Genetics and Pathology Immunology, Genetics and Pathology,SciLifeLab Data Centre

Application that allows users to get predictive data about compound (Single Molecule)

• Hamza Saeed
  Uppsala University Uppsala University,SciLifeLab

  Immunology, Genetics and Pathology Immunology, Genetics and Pathology,SciLifeLab Data Centre

Imminent myocardial infarction prediction model. In patients free from prior cardiovascular disease, we aimed to identify characteristics of an imminent first heart attack and design a prediction model.

• Stefan Gustafsson
  Uppsala University Uppsala University

  Medical Sciences, Clinical Epidemiology Medical Sciences, Clinical Epidemiology

Shiny app for displaying Dictyostelium discoideum RNA-seq and proteomics data, from the publication Edelbroek et al. 2024

• Jakub Westholm
  Stockholms University Stockholms University

  Biochemistry and Biophysics (DBB) Biochemistry and Biophysics (DBB)

Model to predict the pKa of compounds

• Yojana Gadiya
  Fraunhofer Institute for Translational Medicine and Pharmacology Fraunhofer Institute for Translational Medicine and Pharmacology

All the browsable datasets from Lee et al 2024. "Open source, high throughput, targeted in situ transcriptomics"

• Marco Grillo
  Stockholms University Stockholms University

  Biochemistry and Biophysics (DBB) Biochemistry and Biophysics (DBB)

Conformal regression model for predicting LogD for drug-like molecules, trained on ChEMBL version 33 with over 2.2M compounds using the CPSign software.

• Staffan Arvidsson McShane
  Uppsala University Uppsala University

  Pharmaceutical Biosciences Pharmaceutical Biosciences

RepurposeDrugs - an interactive web-based data portal and predictive platform for repurposing mono- and combination therapies.

• Aleksandr Kushnir
  University of Helsinki University of Helsinki

  Public Health and Caring Sciences Public Health and Caring Sciences

Modelling of cell-type signatures in the developmental human heart

• Christophe Avenel
  Uppsala University Uppsala University

  Information Technology Information Technology

Human heart development ISS datasets generated for Lazar et.al 2024.

• Sergio Marco Salas
  Stockholms University Stockholms University

  Biochemistry and Biophysics (DBB) Biochemistry and Biophysics (DBB)

Colorectal cancer usually metastasizes in the liver. Tumor cells can create two types of metastases: desmoplastic (DHGP) or replacement (RHGP). DHGP is characterized by a fibrotic rim that encapsulates the tumor cells and is associated with a better survival. In this project, we found two distinct areas in the rim: an outer area representing a ben ... ign fibrotic reaction, and an inner area modified by the neighboring cancer cells. See more

• Axel Andersson
  Uppsala University Uppsala University

  IT IT

ALLIUM (ALL subtype Identification Using Machine learning) is a multimodal classifier of molecular subtypes in pediatric acute lymphoblastic leukemia, using DNA methylation (DNAm) and gene expression (GEX) data

• Mariya Lysenkova Wiklander
  Uppsala University Uppsala University

  Medical Sciences, SNP&SEQ Technology Platform Medical Sciences, SNP&SEQ Technology Platform

Demo of ROC curves, PR curves, and decision boundaries for teaching purposes, www.henlab.org. By Johan Henriksson. Source at https://github.com/henriksson-lab/demo_roc

• Johan Henriksson
  Umeå University Umeå University

  Molecular Biology Molecular Biology

Demo of xgboost and decision trees for teaching purposes. By Johan Henriksson, www.henlab.org. Source at https://github.com/henriksson-lab/demo_xgboost

• Johan Henriksson
  Umeå University Umeå University

  Molecular Biology Molecular Biology

API for model that predicts water–octanol distribution coefficient (logD) for chemical compounds: It is a proxy for the lipophilicity which is a major determinant of drug properties and overall suitability of drug candidates

• Hamza Saeed
  Uppsala University Uppsala University,SciLifeLab

  Immunology, Genetics and Pathology Immunology, Genetics and Pathology,SciLifeLab Data Centre

Demo of penalized linear models (elastic net) for teaching purposes. By Johan Henriksson, www.henlab.org. Source at https://github.com/henriksson-lab/demo_elasticnet

• Johan Henriksson
  Umeå University Umeå University

  Molecular Biology Molecular Biology

Demo of Bayesian linear models for teaching purposes. By Johan Henriksson, www.henlab.org. Source at https://github.com/henriksson-lab/demo_bayesianlinmod

• Johan Henriksson
  Umeå University Umeå University

  Molecular Biology Molecular Biology

Demo of markov chains and HMMs for teaching purposes. By Johan Henriksson, www.henlab.org. Source at https://github.com/henriksson-lab/demo_markovchain

• Johan Henriksson
  Umeå University Umeå University

  Molecular Biology Molecular Biology

Demo of the Poisson distribution, as relevant for NGS, for teaching purposes, www.henlab.org. By Johan Henriksson. Source at https://github.com/henriksson-lab/demo_poisson

• Johan Henriksson
  Umeå University Umeå University

  Molecular Biology Molecular Biology

Demo of statistical distributions for teaching purposes. By Johan Henriksson, www.henlab.org. Source at https://github.com/henriksson-lab/demo_statdist

• Johan Henriksson
  Umeå University Umeå University

  Molecular Biology Molecular Biology

Co-occurrence plots created using VOS viewer . There are three plots in total, each based on publications from a different SciLifeLab reporting group (i.e. affiliated researchers, infrastructure units, and SciLifeLab fellows). In each plot, we have considered the KeyWords Plus associated with each paper.

• Senthilkumar Panneerselvam
  Uppsala University Uppsala University,SciLifeLab

  Immunology, Genetics and Pathology Immunology, Genetics and Pathology,SciLifeLab Data Centre

An app to check color balance in indexes for sequencing

• Alma Hansen
  Stockholms University Stockholms University,SciLifeLab

  DBB DBB,SciLifeLab National Genomics Infrastructure

Shiny app for exploration of the Genome-wide PeptidoGlycan Profiling dataset of Vibrio cholerae mutant library. Access to this app is password protected while it is under peer review.

• Laura Alvarez
  Umeå University Umeå University

  Molecular Biology Molecular Biology

The mappings are provided for genes, proteins, metabolites, metabolic reactions, diseases, complexes and publications. This is a REST service for programmatic access to BridgeDb content, provided with interactive Swagger documentation using OpenAPI. For more info see https://www.bridgedb.org/.

• Arnold Kochari
  Uppsala University Uppsala University,SciLifeLab

  Genetics, Immunology, and Pathology Genetics, Immunology, and Pathology,SciLifeLab Data Centre

Supplemental interactive visualization of Adipose Tissue Gene expression after exercise. Built using flexdashboard.

• Leonidas Lundell
  Karolinska Institutet Karolinska Institutet

A tool to predict the risk of experiencing refractory/relapse disease within two years in DLBCL patients treated with R-CHOP.

• Hui Wan
  Karolinska Institutet Karolinska Institutet

  Medical Biochemistry and Biophysics, Immunology Medical Biochemistry and Biophysics, Immunology

This Shiny app is used the course CB2030 Systems biology at KTH Royal Instute of Technology.

• Thanadol Sutantiwanichkul
  KTH Royal Institute of Technology KTH Royal Institute of Technology,SciLifeLab

  Systems Biology Systems Biology

CellChat's Shiny app which allows interactive exploration of the cell-cell communication that are analyzed by the CellChat R-package

• Christophe Avenel
  Uppsala University Uppsala University

  Information Technology Information Technology

CoViMAPP (CoViD-19 Meta-Analysis of Plasma Proteins) is a meta-analysis resource of plasma proteins' alterations in COVID-19.

• Haris Babacic
  Karolinska Institutet Karolinska Institutet

  Oncology-Pathology Oncology-Pathology

OmicLoupe server. See https://quantitativeproteomics.org/omicloupe/ for info about OmicLoupe.

• Fredrik Levander
  SciLifeLab SciLifeLab,Lund University

  National Bioinformatics Infrastructure National Bioinformatics Infrastructure

3D igraph from tsne with variable genes (Data from Tiklova et al. 2016)

• Nanjiang Shu
  Uppsala University Uppsala University,SciLifeLab

  Cell and Molecular Biology Cell and Molecular Biology,National Bioinformatics Infrastructure Sweden

Single cell RNA sequencing dataset associated with the manuscript "Amnion signals are essential for mesoderm formation in primates"

• Nanjiang Shu
  Uppsala University Uppsala University,SciLifeLab

  Cell and Molecular Biology Cell and Molecular Biology,National Bioinformatics Infrastructure Sweden

scRNA-seq data in: Small molecule screen identifies a salt-inducible kinase inhibitor inducing β-cell proliferation by transiently activating the unfolded protein response

• Nanjiang Shu
  Uppsala University Uppsala University,SciLifeLab

  Cell and Molecular Biology Cell and Molecular Biology,National Bioinformatics Infrastructure Sweden

Byrnes, Lauren E., et al. Lineage dynamics of murine pancreatic development at single-cell resolution

• Nanjiang Shu
  Uppsala University Uppsala University,SciLifeLab

  Cell and Molecular Biology Cell and Molecular Biology,National Bioinformatics Infrastructure Sweden

The Boreal Rhizospheric Atlas online tool was created to encourage exploration of a metatranscriptomic dataset of Norway spruce fine roots and their associated fungal communities from nutrient limited and nutrient enriched forest plots of the boreal region of Northern Sweden.

• Nicolas Delhomme
  Swedish University of Agricultural Sciences Swedish University of Agricultural Sciences

  Forest Genetics and Plant Physiology Forest Genetics and Plant Physiology